Genetic diversity of rabies virus in Zimbabwe

Rabies is an acute and fatal form of encephalomyelitis caused by rabies virus (RABV) infection. RABV is present throughout the world, particularly in Asia and Africa, in host animals such as domestic dogs. Canine rabies is responsible for thousands human deaths despite existing preventable and prophylactic solutions. RABV is endemic to southern Africa and circulates, in addition to dogs, among wild mammals, livestock and domestic carnivores (e.g. cats), and accidentally in humans. Two different genetic variants of RABV are described in these African regions: Africa 1 lineage, subtype b (AF1b) belonging to the Cosmopolitan clade, and Africa 3 (AF3) clade, associated with the dog and the mongoose, respectively. However, information about the genetic diversity of RABV circulating in Zimbabwe remains limited. In order to bridge this knowledge gap, we analyzed RABV strains present in this country between 2014 and 2020. To this end, brain samples from 50 domestic and 24 wild animal species from different locations in Zimbabwe were collected by the country’s veterinary services. Seventy out of the 74 (94.6%) samples were found positive by direct immunofluorescence. All the samples were also tested by two RT-PCR, targeting L and N genes. Fifty-nine (79.7%) and 28 (37.8%) out the 74 samples tested positive to L gene and N gene respectively, with a total of 62 samples positive to at least one RT-PCR. Phylogenetic analyses demonstrated that the AF1b sub-lineage was predominant, with the co-circulation of two AF1b sub-clustering groups in both domestic animal and wildlife. In addition, the AF3 clade was also detected in two samples. Two nearly complete genomes were also obtained representative of both AF1 sub-lineage and AF3 clades.